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Super-resolution optical imaging | Bioimaging software tools

In recent years, super-resolution optical imaging techniques have been developed to overcome the diffraction limit in fluorescence microscopy (Hell, 2007; Huang et al. 2010). Among these techniques, methods based on stochastic switching and…
SuReSim
Desktop

SuReSim Super Resolution Simulation

A software tool that simulates localization data of arbitrary three-dimensional…

A software tool that simulates localization data of arbitrary three-dimensional structures represented by ground truth models, allowing users to systematically explore how changing experimental…

SR-Tesseler
Desktop

SR-Tesseler

An open-source segmentation software using Voronoï tessellation constructed…

An open-source segmentation software using Voronoï tessellation constructed from the coordinates of localized molecules. It allows precise, robust and automatic quantification of protein…

QuickPALM
Desktop

QuickPALM

A set of programs to aid in the acquisition and image analysis of data in…

A set of programs to aid in the acquisition and image analysis of data in “photoactivated localization microscopy” (PALM) and “stochastic optical reconstruction microscopy” (STORM). QuickPALM…

3B
Desktop

3B Bayesian analysis of blinking and bleaching

Analyses data in which many overlapping fluorophores undergo bleaching and…

Analyses data in which many overlapping fluorophores undergo bleaching and blinking events, giving the structure at enhanced resolution. By using a hidden Markov model (HMM), 3b allows useful…

DAOSTORM
Desktop

DAOSTORM

Provides a more quantitative report of spatial distribution of fluorescent…

Provides a more quantitative report of spatial distribution of fluorescent molecules, to increase quality of super-resolved images of biological samples and to maintain performance at high imaging…

gaussmlev2
Desktop

gaussmlev2

An iterative algorithm that converges to the maximum likelihood estimate of the…

An iterative algorithm that converges to the maximum likelihood estimate of the position and intensity of a single fluorophore. An implementation of the algorithm on graphics processing unit hardware…

rapidSTORM
Desktop

rapidSTORM

A localization microscopy evaluation program. rapidSTORM is designed to find…

A localization microscopy evaluation program. rapidSTORM is designed to find and precisely localize fluorophores in super-resolvable movies such as those generated by the PALM or dSTORM techniques.

ViSP
Desktop

ViSP

An interactive, freely available, cross-platform 3D localization representation…

An interactive, freely available, cross-platform 3D localization representation tool. ViSP advances the interpretation of 3D single-particle super-resolution data (and the features are also…

SRRF
Desktop

SRRF Super-Resolution Radial Fluctuations

Allows to work on both fixed-cell and dynamic live-cell super resolution using…

Allows to work on both fixed-cell and dynamic live-cell super resolution using conventional fluorophores compatible with a variety of imaging modalities. SRRF provides a significant reduction in…

PALMsiever
Desktop

PALMsiever

Provides a user-friendly means of visualizing, filtering and analyzing…

Provides a user-friendly means of visualizing, filtering and analyzing localization microscopy (LM) data. PALMsiever includes drift correction, clustering, intelligent line profiles, many rendering…

SharpViSu
Desktop

SharpViSu

An interactive open-source software with a graphical user interface, which…

An interactive open-source software with a graphical user interface, which allows performing processing steps for localization data in an integrated manner. This includes common features and new…

FOCAL
Desktop

FOCAL Fast Optimized Cluster Algorithm for Localizations

A grid-based clustering algorithm FOCAL, which explicitly accounts for several…

A grid-based clustering algorithm FOCAL, which explicitly accounts for several dominant artifacts arising in SMLM image reconstructions. FOCAL is fast and efficient, scaling like O(n), and only has…

SIMToolbox
Desktop

SIMToolbox

An open-source, modular set of functions for MATLAB equipped with a user…

An open-source, modular set of functions for MATLAB equipped with a user friendly graphical interface and designed for processing 2D and 3D data acquired by structured illumination microscopy. Both…

ThunderSTORM
Desktop

ThunderSTORM

An open-source, interactive and modular plug-in for ImageJ designed for…

An open-source, interactive and modular plug-in for ImageJ designed for automated processing, analysis and visualization of data acquired by single-molecule localization microscopy methods such as…

Angular-Ripleys…
Desktop

Angular-Ripleys-K

Permits to quantitatively assess to fibrous structures in 2D single-molecule…

Permits to quantitatively assess to fibrous structures in 2D single-molecule localization microscopy (SMLM) datasets. Angular-Ripleys-K describes fiber spatial arrangements and shows how these…

iNMF
Desktop

iNMF Non-negative matrix factorisation with iterative restarts

Models a noisy dataset of highly overlapping fluorophores with intermittent…

Models a noisy dataset of highly overlapping fluorophores with intermittent intensities. iNMF enlarges the family of localisation microscopy techniques, and enables using quantum dots as fluorescent…

VirtualMicrosco…
Desktop

VirtualMicroscopy

A real time virtual microscopy technique for interactive analysis of super high…

A real time virtual microscopy technique for interactive analysis of super high resolution microscopic images over internet on standard desktops, laptops or mobile devices. VirtualMicroscopy…

SimpleSTORM
Desktop

SimpleSTORM

Improves the resolution of conventional fluorescent microscopy by one order of…

Improves the resolution of conventional fluorescent microscopy by one order of magnitude. SimpleSTORM is based on a carefully designed yet simple model of the image acquisition process which allows…

FALCON
Desktop

FALCON FAst Localization algorithm based on a CONtinuous-space formulation

Provides unbiased localization on continuous space and high recall rates for…

Provides unbiased localization on continuous space and high recall rates for high-density imaging, and to have orders-of-magnitude shorter run times compared to previous high-density algorithms.…

rainSTORM
Desktop

rainSTORM

A full set of MATLAB routines as a guide to localization image processing.…

A full set of MATLAB routines as a guide to localization image processing. These routines can be used to perform the image processing element of localization microscopy, and includes resolution…

GraspJ
Desktop

GraspJ GPU-Run Analysis for STORM and PALM

An open source, real-time data analysis and rendering tool for super-resolution…

An open source, real-time data analysis and rendering tool for super-resolution imaging techniques that are based on single molecule detection and localization (e.g. stochastic optical reconstruction…

Auto-Bayes
Desktop

Auto-Bayes

A software package based on Bayesian statistics and requires no user dependent…

A software package based on Bayesian statistics and requires no user dependent parameters for molecule detection and image reconstruction for single-molecule localization microscopy (SMLM), including…

Octane
Desktop

Octane

Facilitates works involved in super-resolution optical imaging (PALM, STORM…

Facilitates works involved in super-resolution optical imaging (PALM, STORM etc). By providing an intuitive graphical user interface front end, we hope it can serve as a useful tool for a wide range…

3D-DAOSTORM
Desktop

3D-DAOSTORM

An extension of the DAOPHOT analysis method to the analysis of…

An extension of the DAOPHOT analysis method to the analysis of astigmatism-based 3D super-resolution data where the z position of the emitter is encoded in the x and y width of its point spread…

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